SMTL ID : 6dw5.1

SAMHD1 Bound to Gemcitabine-TP in the Catalytic Pocket

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.93 Å

Oligo State

homo-tetramer

Ligands

4 x GTF: 2'-deoxy-2',2'-difluorocytidine 5'-(tetrahydrogen triphosphate)(Non-covalent)

GTF.1: 18 residues within 4Å: Chain A: Q.73, L.74, R.88, R.130, N.131, H.134, H.139, H.157, D.235, K.236, Y.239, D.243, R.290, H.294, Y.298, Q.299 Ligands: MG.7, MG.8 25 PLIP interactions: 25 interactions with chain A Hydrogen bonds: A:Q.73, A:R.88, A:R.130, A:D.243, A:Q.299 Water bridges: A:R.88, A:R.88, A:R.130, A:R.130, A:H.134, A:H.139, A:R.144, A:D.235, A:Y.298, A:D.307 Salt bridges: A:R.88, A:R.130, A:H.134, A:H.139, A:H.139, A:H.157, A:H.157, A:K.236, A:R.290 pi-Stacking: A:H.139 GTF.9: 17 residues within 4Å: Chain B: Q.73, L.74, R.88, R.130, N.131, H.134, H.139, H.157, D.235, K.236, Y.239, D.243, R.290, H.294, Y.298, Q.299 Ligands: MG.14 25 PLIP interactions: 25 interactions with chain B Hydrogen bonds: B:Q.73, B:R.88, B:Y.239, B:Y.239, B:Y.239, B:D.243, B:Q.299 Water bridges: B:R.88, B:R.88, B:R.130, B:R.130, B:N.131, B:H.139, B:Q.299 Salt bridges: B:R.88, B:R.130, B:R.130, B:H.134, B:H.139, B:H.139, B:H.157, B:H.157, B:K.236, B:R.290 pi-Stacking: B:H.139 GTF.19: 18 residues within 4Å: Chain C: Q.73, L.74, R.88, H.91, R.130, N.131, H.134, H.139, H.157, D.235, K.236, Y.239, D.243, R.290, H.294, Y.298, Q.299 Ligands: NA.20 22 PLIP interactions: 22 interactions with chain C Hydrogen bonds: C:Q.73, C:R.88, C:D.235, C:Y.239, C:D.243, C:Q.299 Water bridges: C:R.130, C:R.130, C:R.130, C:R.130, C:H.139 Salt bridges: C:R.88, C:R.130, C:R.130, C:H.134, C:H.139, C:H.139, C:H.157, C:H.157, C:K.236, C:R.290 pi-Stacking: C:H.139 GTF.23: 19 residues within 4Å: Chain D: Q.73, L.74, R.88, R.130, N.131, H.134, H.139, H.157, D.235, K.236, Y.239, D.243, R.290, H.294, Y.298, Q.299 Ligands: MG.25, MG.26, MG.27 22 PLIP interactions: 22 interactions with chain D Hydrogen bonds: D:Q.73, D:R.88, D:D.243, D:Q.299 Water bridges: D:R.88, D:R.88, D:R.130, D:R.130, D:R.130, D:H.139, D:Y.298, D:Q.299, D:Q.299 Salt bridges: D:R.88, D:R.130, D:H.134, D:H.139, D:H.157, D:H.157, D:K.236, D:R.290 pi-Stacking: D:H.139

4 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

GTP.2: 15 residues within 4Å: Chain A: Y.79, V.80, V.302, R.375 Chain C: K.447 Chain D: K.40, V.41, I.42, I.60, D.61, Q.66, R.69, F.89 Ligands: DTP.16, MG.17 24 PLIP interactions: 7 interactions with chain A, 13 interactions with chain D, 4 interactions with chain C Hydrogen bonds: A:R.375, D:V.41, D:Q.66, D:R.69 Water bridges: A:K.379, A:Y.380, D:K.40, D:K.40, D:K.40, D:K.40, D:D.61, D:Q.66, C:K.447, C:K.447 Salt bridges: A:R.375, A:K.379, A:K.379, D:K.40, D:K.40, D:K.40, D:D.61, C:K.447, C:K.447 pi-Cation interactions: A:R.375 GTP.10: 16 residues within 4Å: Chain B: Y.79, V.80, V.302, R.375, K.379 Chain C: K.40, V.41, I.42, I.60, D.61, Q.66, R.69, F.89 Chain D: K.447 Ligands: MG.18, DTP.22 20 PLIP interactions: 5 interactions with chain B, 12 interactions with chain C, 3 interactions with chain D Hydrogen bonds: B:R.375, C:V.41, C:Q.66, C:R.69 Salt bridges: B:R.375, B:K.379, B:K.379, C:K.40, C:K.40, C:K.40, C:D.61, D:K.447, D:K.447 pi-Cation interactions: B:R.375 Water bridges: C:K.40, C:K.40, C:K.40, C:K.40, C:Q.66, D:K.447 GTP.11: 16 residues within 4Å: Chain A: K.447 Chain B: K.40, V.41, I.42, I.60, D.61, Q.66, R.69, F.89 Chain C: Y.79, V.80, V.302, R.375, K.379 Ligands: DTP.3, MG.4 22 PLIP interactions: 13 interactions with chain B, 7 interactions with chain C, 2 interactions with chain A Hydrogen bonds: B:V.41, B:Q.66, B:R.69, C:R.375 Water bridges: B:K.40, B:K.40, B:K.40, B:K.40, B:D.61, B:Q.66, C:K.301, C:K.379 Salt bridges: B:K.40, B:K.40, B:K.40, B:D.61, C:R.375, C:K.379, C:K.379, A:K.447, A:K.447 pi-Cation interactions: C:R.375 GTP.24: 16 residues within 4Å: Chain A: K.40, V.41, I.42, I.60, D.61, Q.66, R.69, F.89 Chain B: K.447 Chain D: Y.79, V.80, V.302, R.375, K.379 Ligands: MG.5, DTP.12 20 PLIP interactions: 10 interactions with chain A, 8 interactions with chain D, 2 interactions with chain B Hydrogen bonds: A:V.41, A:Q.66, A:R.69, D:R.375 Water bridges: A:K.40, A:K.40, A:D.61, D:K.301, D:K.379, D:K.379 Salt bridges: A:K.40, A:K.40, A:K.40, A:D.61, D:R.375, D:K.379, D:K.379, B:K.447, B:K.447 pi-Cation interactions: D:R.375

4 x DTP: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE(Non-covalent)

DTP.3: 19 residues within 4Å: Chain A: R.257, F.261, R.276, K.278, N.282, K.447 Chain B: V.41, I.42, N.43, H.49 Chain C: V.80, F.81, I.249, R.296, H.300, K.301, V.302 Ligands: MG.4, GTP.11 30 PLIP interactions: 16 interactions with chain A, 12 interactions with chain C, 2 interactions with chain B Hydrogen bonds: A:R.257, A:N.282, C:R.296, B:N.43, B:N.43 Water bridges: A:R.257, A:R.257, A:K.278, A:K.278, A:K.447, A:K.447, C:K.301, C:K.301, C:K.301, C:K.301 Salt bridges: A:R.257, A:R.276, A:K.278, A:K.278, A:K.278, A:K.447, C:H.300, C:H.300, C:K.301, C:K.301, C:K.301 pi-Cation interactions: A:R.257, A:R.257 Hydrophobic interactions: C:V.80, C:F.81 DTP.12: 19 residues within 4Å: Chain A: V.41, I.42, N.43, H.49 Chain B: R.257, F.261, R.276, K.278, N.282, K.447 Chain D: V.80, F.81, I.249, R.296, H.300, K.301, V.302 Ligands: MG.5, GTP.24 28 PLIP interactions: 16 interactions with chain B, 10 interactions with chain D, 2 interactions with chain A Hydrogen bonds: B:R.257, B:N.282, B:N.282, A:N.43, A:N.43 Water bridges: B:R.257, B:R.257, B:R.257, B:R.257, B:R.276, D:K.301, D:K.301, D:K.301 Salt bridges: B:R.257, B:R.276, B:K.278, B:K.278, B:K.278, B:K.447, D:H.300, D:H.300, D:K.301, D:K.301, D:K.301 pi-Cation interactions: B:R.257, B:R.257 Hydrophobic interactions: D:V.80, D:F.81 DTP.16: 16 residues within 4Å: Chain A: V.80, F.81, I.249, R.296, H.300 Chain C: R.257, R.276, K.278, N.282, K.447 Chain D: V.41, I.42, N.43, H.49 Ligands: GTP.2, MG.17 26 PLIP interactions: 2 interactions with chain D, 18 interactions with chain C, 6 interactions with chain A Hydrogen bonds: D:N.43, D:N.43, C:R.257, C:N.282, C:N.282 Water bridges: C:R.257, C:R.257, C:R.276, C:K.278, C:K.278, C:K.447, C:K.447, A:R.296, A:H.300 Salt bridges: C:R.257, C:R.276, C:K.278, C:K.278, C:K.278, C:K.447, A:H.300, A:H.300 pi-Cation interactions: C:R.257, C:R.257 Hydrophobic interactions: A:V.80, A:F.81 DTP.22: 19 residues within 4Å: Chain B: V.80, F.81, I.249, R.296, H.300, K.301, V.302 Chain C: V.41, I.42, N.43, H.49 Chain D: R.257, F.261, R.276, K.278, N.282, K.447 Ligands: GTP.10, MG.18 20 PLIP interactions: 6 interactions with chain B, 12 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: B:V.80, B:F.81 Salt bridges: B:H.300, B:H.300, B:K.301, B:K.301, D:R.257, D:R.276, D:K.278, D:K.278, D:K.278, D:K.447 Hydrogen bonds: D:R.257, D:N.282, D:N.282, C:N.43, C:N.43 Water bridges: D:R.276 pi-Cation interactions: D:R.257, D:R.257

10 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 4 residues within 4Å: Chain A: K.447 Chain B: K.40 Ligands: DTP.3, GTP.11 No protein-ligand interaction detected (PLIP) MG.5: 4 residues within 4Å: Chain A: K.40 Chain B: K.447 Ligands: DTP.12, GTP.24 No protein-ligand interaction detected (PLIP) MG.7: 4 residues within 4Å: Chain A: Y.239, R.290, H.294 Ligands: GTF.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:Y.239 MG.8: 4 residues within 4Å: Chain A: R.130, D.235, Y.239 Ligands: GTF.1 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.235, H2O.2 MG.14: 2 residues within 4Å: Chain B: E.158 Ligands: GTF.9 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.158 MG.17: 4 residues within 4Å: Chain C: K.447 Chain D: K.40 Ligands: GTP.2, DTP.16 No protein-ligand interaction detected (PLIP) MG.18: 4 residues within 4Å: Chain C: K.40 Chain D: K.447 Ligands: GTP.10, DTP.22 No protein-ligand interaction detected (PLIP) MG.25: 3 residues within 4Å: Chain D: D.233, K.236 Ligands: GTF.23 No protein-ligand interaction detected (PLIP) MG.26: 4 residues within 4Å: Chain D: Y.239, R.290, H.294 Ligands: GTF.23 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:H.294 MG.27: 6 residues within 4Å: Chain D: R.88, R.130, N.131, H.134, H.157 Ligands: GTF.23 2 PLIP interactions: 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.134, H2O.22

4 x NA: SODIUM ION(Non-functional Binders)

NA.6: 3 residues within 4Å: Chain A: Q.195, Y.222, S.226 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.226 NA.13: 3 residues within 4Å: Chain B: Q.195, Y.222, S.226 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.222, B:S.226 NA.20: 5 residues within 4Å: Chain C: Y.298, Q.299, N.304, D.307 Ligands: GTF.19 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:D.307, C:D.307 Water bridges: C:R.144 NA.21: 3 residues within 4Å: Chain C: Q.195, Y.222, S.226 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.195

1 x NI: NICKEL (II) ION(Non-covalent)

NI.15: 4 residues within 4Å: Chain B: H.245, H.246 Chain C: H.245, H.246 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Metal complexes: B:H.245, C:H.246

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Knecht, K.M. et al., The structural basis for cancer drug interactions with the catalytic and allosteric sites of SAMHD1. Proc. Natl. Acad. Sci. U.S.A. (2018)

Release Date

2018-10-10

Peptides

Deoxynucleoside triphosphate triphosphohydrolase SAMHD1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Deoxynucleoside triphosphate triphosphohydrolase SAMHD1

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